To answer your specific question...

Information Security is a very, very hot topic in DoD right now. Casual misuse of IT equipment which you have legitimate access to can get your clearance pulled...installing spyware on an ex's computer (assuming it was not joint property at the time) will most likely get his clearance revoked. Not to mention breaking into your house (again assuming it was not joint property)...

Nobody here can really advise you on how to handle it...only you know the guy, your feelings for him, and how much of a threat he might be (if any).

Perhaps have your lawyer call him and explain exactly what is going to happen if he steps out of line again...maybe he will wake up.